Cell Lineage Analysis Research Articles

6873 Expression of Constitutively Active YAP in Murine Gonadotrope Cells Leads to Morphological Alterations and Dysfunction of the Anterior Pituitary Gland

Abstract Disclosure: N. Jakuc: None. M. Bérubé: None. E. Corrêa Dos Santos: None. G. St-Jean: None. M. Paquet: None. U. Boehm: None. D.J. Bernard: None. D.T. Boerboom: None. A. Boyer: None. G. Zamberlam: None. The Hippo transcriptional coactivators, YAP and TAZ, are expressed in cells throughout the anterior pituitary gland in mice. Although the potential physiological roles of YAP and TAZ in gonadotrope cells was unknown, we recently reported that conditional deletion of YAP and TAZ in gonadotrope cells results in increased circulating levels of LH (in males and females) and FSH (males only), and female hyperfertility in mice. Here, to further study the effects of Hippo signaling in gonadotropes, we conditionally expressed a constitutively active YAP (5SA) in these cells using the Cre-lox system with one of two Cre-driver strains, steroidogenic factor-1 (SF-1)-Cre or GnRH receptor-IRES-Cre (GRIC). Such crosses generated two distinct mouse models, which are referred to herein as YAP5SA;SF1-Cre and YAP5SA;GRIC, respectively. Expression of total YAP (YAP5SA and endogenous Yap) and the classic YAP-TEAD target genes, Ctgf, Cyr61, and Ankrd1 was significantly increased in pituitaries of 6-week-old mutant males and females in both the YAP5SA;SF1-Cre and YAP5SA;GRIC models. Animals from both models also showed significantly reduced serum LH and FSH levels as well as lower body mass and gonadosomatic indices when compared to respective controls. Six-week-old male and female mutants from both models showed significant morphological alterations in the pituitary. YAP5SA;SF1-Cre mutants exhibited proliferation of poorly differentiated cells, with high cellular and nuclear atypia with several mitoses. Similarly, YAP5SA;GRIC pituitaries were characterized by an increased number of poorly differentiated cells as well as follicle or papillary-like structure formation and increased cell proliferation and necrosis. Together, these preliminary findings strongly suggest pituitary blastoma or choriocarcinoma, and confirmatory experiments are underway. In light of gross morphological changes that appeared to extend beyond gonadotropes, we performed qPCR analysis of other cell lineages in 6-week-old YAP5SA;GRIC mutants and corresponding controls. Gh, Prl, Tshb, and Pomc mRNA levels were decreased in pituitaries of mutant animals. In addition, GH and ACTH protein expression, as assessed by immunohistochemistry, was nearly undetectable in pituitaries in mutant animals, suggesting compromised presence or function of somatotropes and corticotropes. To better understand the onset of this pathology, we performed histopathological analysis of YAP5SA;GRIC mutants in early post-natal life. Although pituitaries from 1-day-old mutant animals seemed normal in comparison to controls, we found signs of cellular necrosis and vacuolar degeneration in 1-week-old mutants. Together, our results indicate that constitutively active YAP in murine gonadotropes leads to significant morphological and functional alterations throughout the pituitary. Presentation: 6/1/2024

Cellular, Molecular, and Genetic Mechanisms of Avian Beak Development and Evolution.

Diverse research programs employing complementary strategies have been uncovering cellular, molecular, and genetic mechanisms essential to avian beak development and evolution. In reviewing these discoveries, I offer an interdisciplinary perspective on bird beaks that spans their derivation from jaws of dinosaurian reptiles, their anatomical and ecological diversification across major taxonomic groups, their common embryonic origins, their intrinsic patterning processes, and their structural integration. I describe how descriptive and experimental approaches, including gene expression and cell lineage analyses, tissue recombinations, surgical transplants, gain- and loss-of-function methods, geometric morphometrics, comparative genomics, and genome-wide association studies, have identified key constituent parts and putative genes regulating beak morphogenesis and evolution. I focus throughout on neural crest mesenchyme, which generates the beak skeleton and other components, and describe how these embryonic progenitor cells mediate species-specific pattern and link form and function as revealed by 20 years of research using chimeras between quail and duck embryos.

Characterization of Endothelial to Mesenchymal Transition in Air Pollution Mediated Atherosclerosis: Insights from Trajectory Inference and Functional Analyses in Single cell RNA Sequencing Data

Background: Air pollution is the world’s leading environmental risk factor for atherosclerotic cardiovascular disease (ASCVD). Regressive transcriptional reprogramming and transition of cells to primordial states has been identified as a driver of atherosclerosis. Endothelial cell to mesenchymal cell transition (EndoMT) whereby an endothelial cell transforms to a mesenchymal-like cellular phenotype is one such mechanism. However its relevance to air pollution exposure remains uncharacterized. Methods: Male ApoE−/− mice were inhalationally exposed to concentrated particulate matter <2.5μ component (PM2.5) or filtered air (FA, controls) using a Versatile Aerosol Concentration Enrichment System (VACES, 5–6 h/day, 5 d/week for 36 weeks, n = 7/group. PM2.5 concentrations were 70-80 μg/m3 or ~10X ambient levels. Following euthanasia, single-cell RNA-sequencing of aortic cells was performed using the 10-X platform (CA). For all subsequent analyses, aortic cell samples were integrated. Unsupervised clustering (k-NN) and low-dimensional space visualization (UMAP) were performed with a supervised graph method (Minimum Spanning Tree and Principal Curves) to infer and visualize trajectory analysis of novel cell lineages (branching and cell ordering in pseudotime/pseudospace). Functional analyses were carried out by statistical enrichment analysis using Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) against databases of Gene Ontologies (GO), Biological Pathways, putative regulatory motifs, proteins, or disease annotations to find over-representation of terms and functions. Pseudotime distribution assessed along exposure groups and cell-types lineages were statistically compared using GLM models. Differential Expression Analysis within lineages and between groups were tested by GLM and GAM models and FDR correction, followed by functional analyses. Results: Comparison of the pseudotime lineage with lineage root node at the endothelial cells revealed a similarity between observed endothelial (EC) to vascular smooth muscle (VSMC) cell transition with the differential transition noted with PM2.5 from FA. This overlap suggests a potential exaggeration of EC to VSMC transition in response to PM2.5 exposure. Differential gene expression profiling upon PM2.5-exposure in EC revealed significant changes in GO terms related to cell differentiation, cell migration, and regulation of cell population proliferation. Specific genes with variable patterns of expression (4481) were identified along the EC to VSMC lineage. KEGG pathway analysis along the lineage revealed enriched pathways including PI3K/Akt signaling pathway, MAPK signaling pathway, and Rap1 signaling pathway which are all implicated in the development and progression of atherosclerosis. Conclusion: Single-cell analysis reveals that chronic exposure to PM2.5 results in the exaggeration of EC to VSMC transition consistent with the EndoMT paradigm that may help explain the acceleration of ASCVD in response to air pollution exposure. Additional analysis of cell specific pathways may provide improved understanding of mechanisms progression of atherosclerosis in response to environmental exposures. NIH: 1R35ES031702-01, R01 HL155450, 3R35ES031702-02S1; Burroughs Wellcome Fund: 1060485. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Decoding the transcriptional heterogeneity, differentiation lineage, clinical significance in tissue-resident memory CD8 T cell of the small intestine by single-cell analysis

Resident memory T (Trm) cells which are specifically located in non-lymphoid tissues showed distinct phenotypes and functions compared to circulating memory T cells and were vital for the initiation of robust immune response within tissues. However, the heterogeneity in the transcriptional features, development pathways, and cancer response of Trm cells in the small intestine was not demonstrated. Here, we integrated scRNA-seq and scTCR-seq data pan-tissue T cells to explore the heterogeneity of Trm cells and their development pathways. Trm were enriched in tissue-specific immune response and those in the DUO specially interacted with B cells via TNF and MHC-I signatures. T cell lineage analyses demonstrated that Trm might be derived from the T_CD4/CD8 subset within the same organ or migrated from spleen and mesenteric lymph nodes. We compared the immune repertoire of Trm among organs and implied that clonotypes in both DUO and ILE were less expanded and hydrophilic TRB CDR3s were enriched in the DUO. We further demonstrated that Trm in the intestine infiltrated the colorectal cancer and several effector molecules were highly expressed. Finally, the TCGA dataset of colorectal cancer implied that the infiltration of Trm from the DUO and the ILE was beneficial for overall survival and the response to immune checkpoint blockade.

Maternally-Activated Lineage Tracing ( Raeppli ) To Determine Anlagen Size in Drosophila.

We used Raeppli , a sophisticated fluorescent lineage tracing system developed for Drosophila , to map cell clones beginning at the earliest possible stage in development. By expression of the ϕC31 Integrase (the final step in activating lineage marking) in nurse cells and oocytes, we reduced the methodological and biological variation in cell lineage analysis. We characterized the number of cells in fully-developed larval salivary glands, and thereby inferred the number of cells in embryonic anlage, the number of divisions during differentiation, and the variation in clonal behavior. This approach - novel for Raeppli - represents a powerful addition to lineage analysis in Drosophila .

Endosteal stem cells at the bone-blood interface: A double-edged sword for rapid bone formation: Bone marrow endosteal stem cells provide a robust source of bone-making osteoblasts both in normal and abnormal bone formation.

Endosteal stem cells are a subclass of bone marrow skeletal stem cell populations that are particularly important for rapid bone formation occurring in growth and regeneration. These stem cells are strategically located near the bone surface in a specialized microenvironment of the endosteal niche. These stem cells are abundant in young stages but eventually depleted and replaced by other stem cell types residing in a non-endosteal perisinusoidal niche. Single-cell molecular profiling and in vivo cell lineage analyses play key roles in discovering endosteal stem cells. Importantly, endosteal stem cells can transform into bone tumor-making cells when deleterious mutations occur in tumor suppressor genes. The emerging hypothesis is that osteoblast-chondrocyte transitional identities confer a special subset of endosteal stromal cells with stem cell-like properties, which may make them susceptible for tumorigenic transformation. Endosteal stem cells are likely to represent an important therapeutic target of bone diseases caused by aberrant bone formation.

Multi‐modal Imaging‐based peudotime analysis for AD progression

AbstractBackgroundAlzheimer’s disease (AD) progresses along a continuum and begins many years before symptom onset. AD takes a long progression time, making it hard to study the entire spectrum of AD development. Pseudotime analysis widely used in cell lineage analysis have been applied to AD gene expression data to understand the molecular changes along progression. In this work, we performed a neuroimaging‐based pseudotime analysis to explore the progression patterns of different imaging modalities.MethodData were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database (https://adni.loni.usc.edu/). Data from three imaging modalities were collected including MRI (N = 1684), Amyloid (N = 1041), and Tau (N = 540) (Table.1). Out of those, 223 subjects have all three modalities. We tested four different pseudotime analysis tools: PHATE, MONOCLE3, Slingshot, and Destiny. MRI, Amyloid, Tau, and the combined multi‐modality data were used to estimate the pseudotime respectively. Only PHATE returned non‐reversed pseudotime and clear disease trajectoriesResultAmyloid derived pseudotime best captures the continuum of disease progression and differentiate diagnosis groups the best (Fig.1(b,f)). It also showed better correlation with clinical cognition scores than the composite amyloid measure (Fig.2(b,d)). Multi‐modality derived pseudotime reveals turning point of Amyloid and Tau. We found that the accumulation of Amyloid starts to accelerate when the composite SUVR reaches ∼1.2, which agrees well with existing findings (Fig.2(g,h)). Such turning point does not exist for amyloid derived pseudotime. It also reveals temporal order of brain changes within and across modalities (Fig.2(e,f)), where we observed overall amyloid changes starts early (i.e., small pseudotime) and accelerates earlier than overall brain atrophy and Tau deposition. With a closer look into Tau regions, we found Tau deposition in BRAAK 1 regions accumulates in a faster rate than those inBRAAK34 and BRAAK56 regions.ConclusionPseudotime analysis has a great potential for us to better understand the progression of Alzheimer’s disease. New approaches to fully leverage the longitudinal imaging data could provide a refined view of imaging changes and their co‐occurance pattern along AD progression. Longitudinal data in pseudotime analysis could also help capture the subtle changes in very early stage and therefore would likely provide some valuable insights to improve early diagnosis.

Cell lineage analysis reveals signal tracing and compartment characterisation in Drosophila haltere.

Insect halteres, as specialised hind wings, play an important role during aerial manoeuvres. In Drosophila, halteres and wings are homologous appendages with different morphology. Previous studies have focused on the metamorphosis of halteres, while current knowledge about its cell lineage and regional compartmentalization is still limited. In this study, we performed cell-lineage tracing of canonical landmark signals in halteres and present a simple model for haltere development. Cell lineage tracing in wings was used as a reference. The nub showed wing-like expressions in halteres, whereas hth and pnr exhibited different expressions in adult wings and halteres. The lineage tracing revealed that the pouch region gives rise to end-bulb, and hinge cells contribute to proximal haltere formation. Moreover, we demonstrated that twi-expressing cells participate in the cell population of the distal end-bulb. Haematoxylin and eosin staining indicated that muscle cells were present at the distal end-bulb. These results indicated that adult halteres displayed unique cell lineage patterns and the muscle cells are important components of end-bulbs.

Abstract 3131: Anaplastic transformation model in thyroid cancer revealed by single cell lineage and fate analysis

Abstract The deadliest anaplastic thyroid cancer (ATC) often transforms from indolent differentiated thyroid cancer (DTC), however the complex intra-tumor transformation process is poorly understood. We investigated an anaplastic transformation model by dissecting both cell lineage and cell fate transitions using single cell transcriptomes and genetic alterations data of patients with different subtypes of thyroid cancer. The resulting model started from stress-responsive DTC cells to inflammatory ATC cells, to mitotic defective ATC cells and extended all the way to mesenchymal ATC cells. In parallel with tumor cell evolution, macrophages shifted from anti-tumor to tumor-promoting states and T cells reprogrammed from cytotoxic to exhausted states. Further, our analysis identified two important milestones: 1) diploid stage, where ATC cells were commonly diploids with non-RAS mutations and inflammatory phenotypes. 2) aneuploid stage, where ATC cells gained aneuploidy with frequent RAS mutations and mesenchymal phenotypes leading to the extreme lethal stage of ATC progression. Citation Format: Lina Lu, Jennifer Rui Wang, Ying C. Henderson, Shanshan Bai, Jie Yang, Min Hu, Yuanqing Yan, Tuan M Tran, Jianzhuo Li, Cheng-Kai Shiau, Rachel Kieser, Xiao Zhao, Jiping Wang, Roza Nurieva, Michelle D. Williams, Maria E. Cabanillas, Ramona Dadu, Naifa Lamki Busaidy, Mark Zafereo, Nicholas Navin, Stephen Y. Lai, Ruli Gao. Anaplastic transformation model in thyroid cancer revealed by single cell lineage and fate analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3131.

Abstract 136: Single cell lineage analysis reveals clonal evolution and dynamic intra-clonal gene expression states during colorectal cancer progression

Abstract Colorectal cancer harbors heterogeneous cell populations that contribute to tumor progression. Clones with long term tumor-initiating cell activity are thought to fuel colorectal cancer (CRC) metastasis formation and recent reports suggest that drug tolerant persister cells are endowed with the ability to replenish the tumor during relapse upon therapy. To decipher gene expression heterogeneity of sub-populations within individual clones, we link gene expression states to clonal dynamics in metastatic and therapy resistant sub-populations. We transduced CRC patient-derived organoids with CloneTracker XP™ library, which bears stable genetic barcodes expressed on the RNA level. 300,000 uniquely barcoded cells were either passaged with and without drugs treatment (5-fluorouracil, oxaliplatin and irinotecan) in vitro or serially transplanted orthotopically into immune deficient NSG mice. At determined endpoints, cells or xenograft tumors were harvested and analyzed for clonal dynamics and sub-clonal gene expression programs associated to tumor progression and therapy resistance, respectively using single cell RNA and barcode DNA sequencing.Integrated bioinfomatic analyses of scRNA data from more than 35,000 cells before, during and after recovery from in vitro drug treatment linked clonal barcodes to gene expression of individual cells. The clonal complexity score, i.e number of distinct clones/number of cells, remained stable before and after treatment, suggesting that the clonal composition of the cell population was marginally affected by chemotherapy. After recovery, single cell gene expression data reflected that individual clones contain cells in distinct transcriptional states, with an elevated proportion expressing the intestinal stem-like program. In addition, single cell and bulk barcode analysis of transplanted xenografts revealed that the bulk of tumor and metastasis in liver and lung is formed by a subfraction of 0.006% of all transplanted clones, indicating a strong clonal selection. In serial transplantations of metastasis, only 4 to 5 clones constituted more than 90% of cancer cell bulk. Regarding gene expression in tumor, individual cell subpopulations within the same clone were distributed within 12 different gene expression clusters, which were maintained in metastasis. Overall, our results indicate that multiple clones contribute to both metastasis and therapy resistance and suggest that intra-tumoral heterogeneity is driven by modulation of subclonal gene expression programs. Here, we provide insights into subclonal gene expression heterogeneity and identify transcriptional states which may be potentially relevant for tumor progression and therapy resistance. This may provide the basis for the future development and testing of innovative novel treatment strategies directed against these cellular states. Citation Format: M Haidar Kasem, Attila Jády, Jan-Philipp Mallm, Hanno Glimm, Sebastian M. Dieter, Friederike Herbst, Claudia R. Ball. Single cell lineage analysis reveals clonal evolution and dynamic intra-clonal gene expression states during colorectal cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 136.

Origin and diversification of fibroblasts from the sclerotome in zebrafish

Fibroblasts play an important role in maintaining tissue integrity by secreting components of the extracellular matrix and initiating response to injury. Although the function of fibroblasts has been extensively studied in adults, the embryonic origin and diversification of different fibroblast subtypes during development remain largely unexplored. Using zebrafish as a model, we show that the sclerotome, a sub-compartment of the somite, is the embryonic source of multiple fibroblast subtypes including tenocytes (tendon fibroblasts), blood vessel associated fibroblasts, fin mesenchymal cells, and interstitial fibroblasts. High-resolution imaging shows that different fibroblast subtypes occupy unique anatomical locations with distinct morphologies. Long-term Cre-mediated lineage tracing reveals that the sclerotome also contributes to cells closely associated with the axial skeleton. Ablation of sclerotome progenitors results in extensive skeletal defects. Using photoconversion-based cell lineage analysis, we find that sclerotome progenitors at different dorsal-ventral and anterior-posterior positions display distinct differentiation potentials. Single-cell clonal analysis combined with in vivo imaging suggests that the sclerotome mostly contains unipotent and bipotent progenitors prior to cell migration, and the fate of their daughter cells is biased by their migration paths and relative positions. Together, our work demonstrates that the sclerotome is the embryonic source of trunk fibroblasts as well as the axial skeleton, and local signals likely contribute to the diversification of distinct fibroblast subtypes.

Mouse vaginal development with lateral enlargement at late embryonic stages and caudal elongation after birth.

Müllerian ducts give rise to the oviducts, uterus, cervix, and vagina. During female reproductive tract development in mice, the bilateral Müllerian duct epithelium grows caudally until reaching the urogenital sinus epithelium. This is followed by further caudal growth with the reduction of the urogenital sinus epithelium. Finally, the vaginal epithelium of adult mice is entirely derived from the Müllerian duct epithelium. Here, we explored the mechanisms underlying mouse vaginal development via cell proliferation, apoptosis, and lineage analyses. We found that at the late embryonic stages, apoptosis occurred at the attachment site of bilateral Müllerian duct epithelia below the cervix, resulting in bilateral lumen traffic. The Müllerian duct epithelium was enclosed by the urogenital sinus epithelium at their boundary region on embryonic day (E) 16.5, whereas the Müllerian duct epithelium encased the urogenital sinus epithelium at postnatal day (P) 0 through lateral enlargement. Lateral Müllerian duct enlargement was accompanied by focal ERK activation within the curved epithelial tips and the specific localization of mitotic nuclei on the luminal side of the Müllerian duct epithelial layer at E17.5. Descent of the Müllerian duct epithelium and shortening of the urogenital sinus epithelium occurred rapidly after birth, accompanied by cell proliferation in the Müllerian duct epithelium and its peripheral mesenchymal tissues as well as intense apoptosis in the urogenital sinus epithelium around their boundary region. Urogenital sinus epithelium was localized at the base of the vagina at P7. In conclusion, the mouse vagina develops laterally at the late embryonic stages and caudally after birth.

Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis.

Noise plays a major role in cellular processes and in the development of tissues and organs. Several studies have examined the origin, the integration or the accommodation of noise in gene expression, cell growth and elaboration of organ shape. By contrast, much less is known about variability in cell division plane positioning, its origin and links with cell geometry, and its impact on tissue organization. Taking advantage of the first-stereotyped-then-variable division patterns in the embryo of the model plant Arabidopsis thaliana, we combined 3D imaging and quantitative cell shape and cell lineage analysis together with mathematical and computer modeling to perform a large-scale, systematic analysis of variability in division plane orientation. Our results reveal that, paradoxically, variability in cell division patterns of Arabidopsis embryos is accompanied by a progressive reduction of heterogeneity in cell shape topology. The paradox is solved by showing that variability operates within a reduced repertoire of possible division plane orientations that is related to cell geometry. We show that in several domains of the embryo, a recently proposed geometrical division rule recapitulates observed variable patterns, suggesting that variable patterns emerge from deterministic principles operating in a variable geometrical context. Our work highlights the importance of emerging patterns in the plant embryo under iterated division principles, but also reveal domains where deviations between rule predictions and experimental observations point to additional regulatory mechanisms.

The fate of early perichondrial cells in developing bones

In endochondral bone development, bone-forming osteoblasts and bone marrow stromal cells have dual origins in the fetal cartilage and its surrounding perichondrium. However, how early perichondrial cells distinctively contribute to developing bones remain unidentified. Here we show using in vivo cell-lineage analyses that Dlx5+ fetal perichondrial cells marked by Dlx5-creER do not generate cartilage but sustainably contribute to cortical bone and marrow stromal compartments in a manner complementary to fetal chondrocyte derivatives under the regulation of Hedgehog signaling. Postnatally, Dlx5+ fetal perichondrial cell derivatives preferentially populate the diaphyseal marrow stroma with a dormant adipocyte-biased state and are refractory to parathyroid hormone-induced bone anabolism. Therefore, early perichondrial cells of the fetal cartilage are destined to become an adipogenic subset of stromal cells in postnatal diaphyseal bone marrow, supporting the theory that the adult bone marrow stromal compartments are developmentally prescribed within the two distinct cells-of-origins of the fetal bone anlage.

Transcriptome profile and clinical characterization of ICOS expression in gliomas.

Inducible co-stimulator (ICOS), an immune costimulatory molecule, has been found to play an essential role across various malignancies. This study investigated the transcriptome profile and clinical characterization of ICOS in gliomas. Clinical information and transcriptome data of 301 glioma samples were downloaded from the Chinese Glioma Genome Atlas (CGGA) dataset for analysis (CGGA301 cohort). Furthermore, the results were validated in 697 samples with RNAseq data from the TCGA glioma dataset and 325 gliomas with RNAseq data from the CGGA325 dataset. Immunohistochemistry was performed to evaluate ICOS protein expression across different WHO grades in a tissue microarray (TMA). In addition, single-cell sequencing data from CGGA and GSE 163108 datasets were used to analyze the ICOS expression across different cell types. Statistical analyses and figure production were performed with R-language. We found that ICOS was significantly upregulated in higher-grade, IDH wild type, and mesenchymal subtype of gliomas. Functional enrichment analyses revealed that ICOS was mainly involved in glioma-related immune response. Moreover, ICOS showed a robust correlation with other immune checkpoints, including the PD1/PD-L1/PD-L2 pathway, CTLA4, ICOSL (ICOS ligand), and IDO1. Subsequent Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed that GBM patients with higher ICOS expression seemed to be more sensitive to ICB therapy. Furthermore, based on seven clusters of metagenes, GSVA identified that ICOS was tightly associated with HCK, LCK, MHC-I, MHC-II, STAT1, and interferon, especially with LCK, suggesting a strong correlation between ICOS and T-cell activity in gliomas. In cell lineage analysis, Higher-ICOS gliomas tended to recruit dendritic cells, monocytes, and macrophages into the tumor microenvironment. Single-cell sequencing analysis indicated that ICOS was highly expressed by regulatory T cells (Tregs), especially in mature Tregs. Finally, patients with higher ICOS had shortened survival. ICOS was an independent prognosticator for glioma patients. In conclusion, higher ICOS is correlated with more malignancy of gliomas and is significantly associated with Treg activity among glioma-related immune responses. Moreover, ICOS could contribute as an independent prognostic factor for gliomas. Our study highlights the role of ICOS in glioma and may facilitate therapeutic strategies targeting ICOS for glioma.

A detailed redescription of the mesoderm/neural crest cell boundary in the murine orbitotemporal region integrates the mammalian cranium into a pan-amniote cranial configuration.

The morphology of the mammalian chondrocranium appears to differ significantly from those of other amniotes, since the former possesses uniquely developed brain and cranial sensory organs. In particular, a question has long remained unanswered as to the developmental and evolutionary origins of a cartilaginous nodule called the ala hypochiasmatica. In this study, we investigated the embryonic origin of skeletal elements in the murine orbitotemporal region by combining genetic cell lineage analysis with detailed morphological observation. Our results showed that the mesodermal embryonic environment including the ala hypochiasmatica, which appeared as an isolated mesodermal distribution in the neural crest-derived prechordal region, is formed as a part of the mesoderm that continued from the chordal region during early chondrocranial development. The mesoderm/neural crest cell boundary in the head mesenchyme is modified through development, resulting in the secondary mesodermal expansion to invade into the prechordal region. We thus revealed that the ala hypochiasmatica develops as the frontier of the mesodermal sheet stretched along the cephalic flexure. These results suggest that the mammalian ala hypochiasmatica has evolved from a part of the mesodermal primary cranial wall in ancestral amniotes. In addition, the endoskeletal elements in the orbitotemporal region, such as the orbital cartilage, suprapterygoid articulation of the palatoquadrate, and trabecula, some of which were once believed to represent primitive traits of amniotes and to be lost in the mammalian lineage, have been confirmed to exist in the mammalian cranium. Consequently, the mammalian chondrocranium can now be explained in relation to the pan-amniote cranial configuration.

Prediction of lung cancer immunotherapy response via machine learning analysis of immune cell lineage and surface markers

Although advances have been made in cancer immunotherapy, patient benefits remain elusive. For non-small cell lung cancer (NSCLC), monoclonal antibodies targeting programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) have shown survival benefit compared to chemotherapy. Personalization of treatment would be facilitated by a priori identification of patients likely to benefit. This pilot study applied a suite of machine learning methods to analyze mass cytometry data of immune cell lineage and surface markers from blood samples of a small cohort (n= 13) treated with Pembrolizumab, Atezolizumab, Durvalumab, or Nivolumab as monotherapy. Four different comparisons were evaluated between data collected at an initial visit (baseline), after 12-weeks of immunotherapy, and from healthy (control) samples: healthy vs patients at baseline, Responders vs Non-Responders at baseline, Healthy vs 12-week Responders, and Responders vs Non-Responders at 12-weeks. The algorithms Random Forest, Partial Least Squares Discriminant Analysis, Multi-Layer Perceptron, and Elastic Net were applied to find features differentiating between these groups and provide for the capability to predict outcomes. Particular combinations and proportions of immune cell lineage and surface markers were sufficient to accurately discriminate between the groups without overfitting the data. In particular, markers associated with the B-cell phenotype were identified as key features. This study illustrates a comprehensive machine learning analysis of circulating immune cell characteristics of NSCLC patients with the potential to predict response to immunotherapy. Upon further evaluation in a larger cohort, the proposed methodology could help guide personalized treatment selection in clinical practice.

Cranial Base Synchondrosis Lacks PTHrP-Expressing Column-Forming Chondrocytes.

The cranial base contains a special type of growth plate termed the synchondrosis, which functions as the growth center of the skull. The synchondrosis is composed of bidirectional opposite-facing layers of resting, proliferating, and hypertrophic chondrocytes, and lacks the secondary ossification center. In long bones, the resting zone of the epiphyseal growth plate houses a population of parathyroid hormone-related protein (PTHrP)-expressing chondrocytes that contribute to the formation of columnar chondrocytes. Whether PTHrP+ chondrocytes in the synchondrosis possess similar functions remains undefined. Using Pthrp-mCherry knock-in mice, we found that PTHrP+ chondrocytes predominantly occupied the lateral wedge-shaped area of the synchondrosis, unlike those in the femoral growth plate that reside in the resting zone within the epiphysis. In vivo cell-lineage analyses using a tamoxifen-inducible Pthrp-creER line revealed that PTHrP+ chondrocytes failed to establish columnar chondrocytes in the synchondrosis. Therefore, PTHrP+ chondrocytes in the synchondrosis do not possess column-forming capabilities, unlike those in the resting zone of the long bone growth plate. These findings support the importance of the secondary ossification center within the long bone epiphysis in establishing the stem cell niche for PTHrP+ chondrocytes, the absence of which may explain the lack of column-forming capabilities of PTHrP+ chondrocytes in the cranial base synchondrosis.

Retroviral lineage analysis reveals dual contribution from ectodermal placodes and neural crest cells to avian olfactory sensory and GnRH neurons.

The origin of the neurons and glia in the olfactory system of vertebrates has been controversial, with different cell types attributed to being of ectodermal placode versus neural crest lineage, depending upon the species. Here, we use replication incompetent avian (RIA) retroviruses to perform prospective cell lineage analysis of either presumptive olfactory placode or neural crest cells during early development of the chick embryo. Surprisingly, the results reveal a dual contribution from both the olfactory placode and neural crest cells to sensory neurons in the nose and Gonadotropin Releasing Hormone (GnRH) neurons migrating to the olfactory bulb. We also confirm that olfactory ensheathing glia are solely derived from the neural crest. Finally, our results show that neural crest cells and olfactory placode cells contribute to p63 positive cells, likely to be basal stem cells of the olfactory epithelium. Taken together, these finding provide evidence for previously unknown contributions of neural crest cells to some cell types in the chick olfactory system and help resolve previous discrepancies in the literature.

Defining the Hoxb8 cell lineage during murine definitive hematopoiesis.

ABSTRACTPreviously, we have demonstrated that a subpopulation of microglia, known as Hoxb8 microglia, is derived from the Hoxb8 lineage during the second wave (E8.5) of yolk sac hematopoiesis, whereas canonical non-Hoxb8 microglia arise from the first wave (E7.5). Hoxb8 microglia have an ontogeny distinct from non-Hoxb8 microglia. Dysfunctional Hoxb8 microglia cause the acquisition of chronic anxiety and an obsessive-compulsive spectrum-like behavior, trichotillomania, in mice. The nature and fate of the progenitors generated during E8.5 yolk sac hematopoiesis have been controversial. Herein, we use the Hoxb8 cell lineage reporter to define the ontogeny of hematopoietic cells arising during the definitive waves of hematopoiesis initiated in the E8.5 yolk sac and aorta-gonad-mesonephros (AGM) region. Our murine cell lineage analysis shows that the Hoxb8 cell lineage reporter robustly marks erythromyeloid progenitors, hematopoietic stem cells and their progeny, particularly monocytes. Hoxb8 progenitors and microglia require Myb function, a hallmark transcription factor for definitive hematopoiesis, for propagation and maturation. During adulthood, all immune lineages and, interestingly, resident macrophages in only hematopoietic/lymphoid tissues are derived from Hoxb8 precursors. These results illustrate that the Hoxb8 lineage exclusively mirrors murine definitive hematopoiesis.